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Gene Logic, Affymetrix, Nanosphere, Fujifilm

Gene Logic has received US Patent No. 7,251,642, “Analysis engine and work space manager for use with gene expression data.” The patent describes a platform for managing, integrating, and analyzing gene expression data. According to the patent’s abstract, the platform includes a run time engine that provides more direct, quicker, and more efficient access to gene expression data through the use of memory mapped files. The platform also includes a workspace that is implemented in directories with data objects comprising XML descriptors coupled with binary data objects for storing gene and sample identifiers and input parameters for saved analysis sessions, the abstract states. Finally, the platform provides various application programming interfaces to a data warehouse, including a low-level C++ API, a high-level C++ API, a Perl API, an R API, and a CORBA API to access gene expression data from RTE memory mapped files.

Affymetrix has received US Patent No. 7,250,289, “Methods of genetic analysis of mouse.” The patent claims nucleic acid sequences that are complementary to a wide variety of mouse genes. The patent also provides the sequences in such a way as to make them available for a variety of analyses, such as an array of probes that may be used to measure gene expression of at least 30,000 mouse genes.

Nanosphere of Northbrook, Ill., has received US Patent No. 7,250,499, “Nanoparticles having oligonucleotides attached thereto and uses therefor.” The patent claims methods of detecting a nucleic acid by contacting the nucleic acid with one or more types of particles having oligonucleotides attached. In one embodiment of the method, the oligonucleotides are attached to nanoparticles and have sequences complementary to portions of the sequence of the nucleic acid. A detectable change is then brought about as a result of the hybridization of the oligonucleotides
on the nanoparticles to the nucleic acid.

Fujifilm of Tokyo has received US Patent No. 7,250,257, “Method of detecting mismatching regions.” The patent describes a method where a labeled polynucleotide is subjected to hybridization with oligonucleotide probes fixed respectively to regions on a supporting material. With a first restriction enzyme, a single-stranded moiety of the labeled polynucleotide is first separated from a double strand having been formed by the labeled polynucleotide and each probe. First detection data is then obtained from each region. Next, a mismatching moiety, at which the labeled polynucleotide and a certain probe have undergone a mismatch binding, is separated with a second restriction enzyme, and second detection data is obtained from each region. The region to which the mismatch polynucleotide was bound is finally specified in accordance with results of a comparison between the first detection data and the second detection data, the patent’s abstract states.